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Hi,
the following things would be good to see on a hg38 track, to give people an idea how HPRC relates to the reference genome. The goal is that a genetics curator can see "does HPRC have anything …
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Reading in vcfs from variant callers that run on long-read bams is only part of the problem. MAVIS still needs bam files for most operations. Such bams have a few key differences from short-read ("NGS…
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Dear @mnshgl0110,
I hope this message finds you well. I am reaching out to you because I am currently utilizing Syri, which I find to be an exceptionally useful tool for calling structural variants (…
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Hello @jiadong324,
Thank you for developing such an excellent tool. I have used SVision to detect tandem repeat variations in the HG002 sample with the GRCh38 reference. I employed the default comm…
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Fathom currently has anonymous product types (records), but no (convenient) way of expressing sum types.
# Potential solutions
* Do nothing. Encode sum types as dependent records (eg `let Option :…
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Hello Galaxy Devs
I would like to suggest the idea of adding structural variant analysis tools onto Galaxy Main.
Currently, there are tools for detecting small variants, but those are for less than …
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I've added a dropdown field into the REDCap variant form with two options - SNV and CNV
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Do vg filter out some variants during the construction of the pan-genome, and if so, what are the criteria for filtering? The number of variations in the pan-genome is reduced compared to the variatio…
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Hello,
I've noticed that some variants are reported as PRECISE and with a PASS filter but when taking a look at the alignment in the IGV the position reported is wrong in comparison to the actual p…
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Hi,
I am using Lumpy to find structural variants. While reading paper I came across using 1000 genome SVs as a priors to use with Lumpy. I was trying to understand more about how to use priors with lu…